I've tried this on my personal Trunk Notes installation and on an out of the box installation, however I've been unable to reproduce your problem.
Special:Header, Special:Footer and Special:Badge are installed by Trunk Notes when first run, it should then allow those to be edited. You cannot however add Special: pages yourself. The Special:SetStyleSheet is created when you turn on custom stylesheets in the Settings.
If, when viewing pages, you tap in the search bar at the top you should be able to start typing in Special and see the Special:Header, etc pages. If not then something has gone wrong.
One thing to try is creating the files Special:Header, Special:Footer and Special:Badge on your computer, zipping them up and then uploading to Trunk Notes. If you cannot create those files because you are using Windows (which has a large number of special characters it doesn't like in filenames) then create each file without the : but include on the first line of the file the text "Title: Special:Header", etc
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